Examples with SimpleQuantity org.hl7.fhir.dstu2016may.model.SimpleQuantity used on opensource projects

Example 6 with SimpleQuantity

use of org.hl7.fhir.dstu2016may.model.SimpleQuantity in project kindling by HL7.

the class JsonLDDefinitionsGenerator method generate.

// private String genDate;
// private String version;
// private BuildWorkerContext workerContext;
public void generate(Definitions definitions, IniFile ini, String tmpResDir, String dstDir, String srcDir, FHIRVersion version, String genDate, BuildWorkerContext workerContext) throws Exception {
    // this.genDate = genDate;
    // this.version = version;
    // this.workerContext = workerContext;
    JsonObject defn = new JsonObject();
    JsonObject context = new JsonObject();
    defn.add("@context", context);
    defn.addProperty("@id", "http://hl7.org/fhir/");
    context.addProperty("fhir", "http://hl7.org/fhir/");
    context.addProperty("xsd", "http://www.w3.org/2001/XMLSchema#");
    // properties for primitives, helpers, format features
    addProperty(context, "value", "fhir:value", "xsd:string");
    addProperty(context, "decimal", "fhir:value", "xsd:decimal");
    addProperty(context, "integer", "fhir:value", "xsd:integer");
    if (!version.isR4B()) {
        addProperty(context, "integer64", "fhir:value", "xsd:string");
    }
    addProperty(context, "boolean", "fhir:value", "xsd:boolean");
    addProperty(context, "binary", "fhir:value", "xsd:base64Binary");
    addProperty(context, "date", "fhir:value", "xsd:date");
    addProperty(context, "dateTime", "fhir:value", "xsd:dateTime");
    addProperty(context, "gYearMonth", "fhir:value", "xsd:gYearMonth");
    addProperty(context, "gYear", "fhir:value", "xsd:gYear");
    addProperty(context, "link", "fhir:link", "@id");
    addProperty(context, "concept", "fhir:concept", "@id");
    addProperty(context, "index", "fhir:index", "xsd:integer");
    addProperty(context, "role", "fhir:nodeRole", "@id");
    // elements defined in FHIR:
    for (TypeRef tr : definitions.getKnownTypes()) {
        if (!definitions.hasPrimitiveType(tr.getName()) && !tr.getName().equals("SimpleQuantity") && !tr.getName().equals("MoneyQuantity")) {
            TypeDefn root = definitions.getElementDefn(tr.getName());
            new JsonLDGenerator(definitions, workerContext, definitions.getKnownTypes()).generate(context, root, version, genDate);
        }
    }
    List<String> names = new ArrayList<String>();
    names.addAll(definitions.getResources().keySet());
    names.addAll(definitions.getBaseResources().keySet());
    names.add("Parameters");
    Collections.sort(names);
    for (String name : names) {
        ResourceDefn root = definitions.getResourceByName(name);
        new JsonLDGenerator(definitions, workerContext, definitions.getKnownTypes()).generate(context, root.getRoot(), version, genDate);
    }
    save(defn, dstDir + "fhir.jsonld");
}

Example 7 with SimpleQuantity

use of org.hl7.fhir.dstu2016may.model.SimpleQuantity in project kindling by HL7.

the class FhirTurtleGenerator method processTypes.

private void processTypes(String baseResourceName, FHIRResource baseResource, ElementDefn td, String predicateBase, boolean innerIsBackbone) throws Exception {
    for (ElementDefn ed : td.getElements()) {
        String predicateName = predicateBase + "." + (ed.getName().endsWith("[x]") ? ed.getName().substring(0, ed.getName().length() - 3) : ed.getName());
        FHIRResource predicateResource;
        if (ed.getName().endsWith("[x]")) {
            predicateResource = fact.fhir_objectProperty(predicateName);
            // Choice entry
            if (ed.typeCode().equals("*")) {
                // Wild card -- any element works (probably should be more restrictive but...)
                Resource targetResource = RDFNamespace.FHIR.resourceRef("Element");
                baseResource.restriction(fact.fhir_cardinality_restriction(predicateResource.resource, targetResource, ed.getMinCardinality(), ed.getMaxCardinality()));
                predicateResource.domain(baseResource);
                predicateResource.range(targetResource);
            } else {
                // Create a restriction on the union of possible types
                List<Resource> typeOpts = new ArrayList<Resource>();
                for (TypeRef tr : ed.getTypes()) {
                    // TODO: Figure out how to get the type reference code
                    String trName = tr.getName();
                    if (trName.equals("SimpleQuantity"))
                        trName = "Quantity";
                    String qualifiedPredicateName = predicateName + Utilities.capitalize(trName);
                    Resource targetRes = fact.fhir_class(tr.getName()).resource;
                    FHIRResource qualifiedPredicate = fact.fhir_objectProperty(qualifiedPredicateName, predicateResource.resource).domain(baseResource).range(targetRes);
                    typeOpts.add(fact.fhir_cardinality_restriction(qualifiedPredicate.resource, targetRes, ed.getMinCardinality(), ed.getMaxCardinality()));
                }
                baseResource.restriction(fact.fhir_union(typeOpts));
            }
        } else {
            FHIRResource baseDef;
            if (ed.getTypes().isEmpty()) {
                predicateResource = fact.fhir_objectProperty(predicateName);
                String targetClassName = mapComponentName(baseResourceName, ed.getDeclaredTypeName());
                baseDef = fact.fhir_class(targetClassName, innerIsBackbone ? "BackboneElement" : "Element").addDefinition(ed.getDefinition());
                processTypes(targetClassName, baseDef, ed, predicateName, innerIsBackbone);
            } else {
                TypeRef targetType = ed.getTypes().get(0);
                String targetName = targetType.getName();
                if (targetName.startsWith("@")) {
                    // Link to earlier definition
                    ElementDefn targetRef = getElementForPath(targetName.substring(1));
                    String targetRefName = targetRef.getName();
                    String targetClassName = baseResourceName + Character.toUpperCase(targetRefName.charAt(0)) + targetRefName.substring(1);
                    baseDef = fact.fhir_class(targetClassName, innerIsBackbone ? "BackboneElement" : "Element").addDefinition(ed.getDefinition()).addTitle(ed.getShortDefn());
                    if (!processing.contains(targetRefName)) {
                        processing.add(targetRefName);
                        processTypes(targetClassName, baseDef, targetRef, predicateName, innerIsBackbone);
                        processing.remove(targetRefName);
                    }
                } else {
                    // A placeholder entry.  The rest of the information will be supplied elsewhere
                    baseDef = fact.fhir_class(targetName);
                }
                // XHTML the exception, in that the html doesn't derive from Primitive
                if (targetName.equals("xhtml"))
                    predicateResource = fact.fhir_dataProperty(predicateName);
                else
                    predicateResource = fact.fhir_objectProperty(predicateName);
            }
            predicateResource.addTitle(ed.getShortDefn()).addDefinition(ed.getDefinition()).domain(baseResource);
            baseResource.restriction(fact.fhir_cardinality_restriction(predicateResource.resource, baseDef.resource, ed.getMinCardinality(), ed.getMaxCardinality()));
            predicateResource.range(baseDef.resource);
            if (!Utilities.noString(ed.getW5()))
                predicateResource.addObjectProperty(RDFS.subPropertyOf, RDFNamespace.W5.resourceRef(ed.getW5()));
        }
    }
}

Example 8 with SimpleQuantity

use of org.hl7.fhir.dstu2016may.model.SimpleQuantity in project org.hl7.fhir.core by hapifhir.

the class JsonParser method composeType.

protected void composeType(String prefix, Type type) throws IOException {
    if (type == null)
        ;
    else if (type instanceof Age)
        composeAge(prefix + "Age", (Age) type);
    else if (type instanceof Count)
        composeCount(prefix + "Count", (Count) type);
    else if (type instanceof Money)
        composeMoney(prefix + "Money", (Money) type);
    else if (type instanceof Distance)
        composeDistance(prefix + "Distance", (Distance) type);
    else if (type instanceof Duration)
        composeDuration(prefix + "Duration", (Duration) type);
    else if (type instanceof SimpleQuantity)
        composeSimpleQuantity(prefix + "SimpleQuantity", (SimpleQuantity) type);
    else if (type instanceof Period)
        composePeriod(prefix + "Period", (Period) type);
    else if (type instanceof Coding)
        composeCoding(prefix + "Coding", (Coding) type);
    else if (type instanceof Range)
        composeRange(prefix + "Range", (Range) type);
    else if (type instanceof Quantity)
        composeQuantity(prefix + "Quantity", (Quantity) type);
    else if (type instanceof Attachment)
        composeAttachment(prefix + "Attachment", (Attachment) type);
    else if (type instanceof Ratio)
        composeRatio(prefix + "Ratio", (Ratio) type);
    else if (type instanceof Annotation)
        composeAnnotation(prefix + "Annotation", (Annotation) type);
    else if (type instanceof SampledData)
        composeSampledData(prefix + "SampledData", (SampledData) type);
    else if (type instanceof Reference)
        composeReference(prefix + "Reference", (Reference) type);
    else if (type instanceof CodeableConcept)
        composeCodeableConcept(prefix + "CodeableConcept", (CodeableConcept) type);
    else if (type instanceof Identifier)
        composeIdentifier(prefix + "Identifier", (Identifier) type);
    else if (type instanceof Signature)
        composeSignature(prefix + "Signature", (Signature) type);
    else if (type instanceof TriggerDefinition)
        composeTriggerDefinition(prefix + "TriggerDefinition", (TriggerDefinition) type);
    else if (type instanceof ElementDefinition)
        composeElementDefinition(prefix + "ElementDefinition", (ElementDefinition) type);
    else if (type instanceof Timing)
        composeTiming(prefix + "Timing", (Timing) type);
    else if (type instanceof ModuleMetadata)
        composeModuleMetadata(prefix + "ModuleMetadata", (ModuleMetadata) type);
    else if (type instanceof ActionDefinition)
        composeActionDefinition(prefix + "ActionDefinition", (ActionDefinition) type);
    else if (type instanceof Address)
        composeAddress(prefix + "Address", (Address) type);
    else if (type instanceof HumanName)
        composeHumanName(prefix + "HumanName", (HumanName) type);
    else if (type instanceof DataRequirement)
        composeDataRequirement(prefix + "DataRequirement", (DataRequirement) type);
    else if (type instanceof Meta)
        composeMeta(prefix + "Meta", (Meta) type);
    else if (type instanceof ParameterDefinition)
        composeParameterDefinition(prefix + "ParameterDefinition", (ParameterDefinition) type);
    else if (type instanceof ContactPoint)
        composeContactPoint(prefix + "ContactPoint", (ContactPoint) type);
    else if (type instanceof MarkdownType) {
        composeMarkdownCore(prefix + "Markdown", (MarkdownType) type, false);
        composeMarkdownExtras(prefix + "Markdown", (MarkdownType) type, false);
    } else if (type instanceof UnsignedIntType) {
        composeUnsignedIntCore(prefix + "UnsignedInt", (UnsignedIntType) type, false);
        composeUnsignedIntExtras(prefix + "UnsignedInt", (UnsignedIntType) type, false);
    } else if (type instanceof CodeType) {
        composeCodeCore(prefix + "Code", (CodeType) type, false);
        composeCodeExtras(prefix + "Code", (CodeType) type, false);
    } else if (type instanceof IdType) {
        composeIdCore(prefix + "Id", (IdType) type, false);
        composeIdExtras(prefix + "Id", (IdType) type, false);
    } else if (type instanceof OidType) {
        composeOidCore(prefix + "Oid", (OidType) type, false);
        composeOidExtras(prefix + "Oid", (OidType) type, false);
    } else if (type instanceof PositiveIntType) {
        composePositiveIntCore(prefix + "PositiveInt", (PositiveIntType) type, false);
        composePositiveIntExtras(prefix + "PositiveInt", (PositiveIntType) type, false);
    } else if (type instanceof UuidType) {
        composeUuidCore(prefix + "Uuid", (UuidType) type, false);
        composeUuidExtras(prefix + "Uuid", (UuidType) type, false);
    } else if (type instanceof IntegerType) {
        composeIntegerCore(prefix + "Integer", (IntegerType) type, false);
        composeIntegerExtras(prefix + "Integer", (IntegerType) type, false);
    } else if (type instanceof DateTimeType) {
        composeDateTimeCore(prefix + "DateTime", (DateTimeType) type, false);
        composeDateTimeExtras(prefix + "DateTime", (DateTimeType) type, false);
    } else if (type instanceof DateType) {
        composeDateCore(prefix + "Date", (DateType) type, false);
        composeDateExtras(prefix + "Date", (DateType) type, false);
    } else if (type instanceof DecimalType) {
        composeDecimalCore(prefix + "Decimal", (DecimalType) type, false);
        composeDecimalExtras(prefix + "Decimal", (DecimalType) type, false);
    } else if (type instanceof UriType) {
        composeUriCore(prefix + "Uri", (UriType) type, false);
        composeUriExtras(prefix + "Uri", (UriType) type, false);
    } else if (type instanceof Base64BinaryType) {
        composeBase64BinaryCore(prefix + "Base64Binary", (Base64BinaryType) type, false);
        composeBase64BinaryExtras(prefix + "Base64Binary", (Base64BinaryType) type, false);
    } else if (type instanceof TimeType) {
        composeTimeCore(prefix + "Time", (TimeType) type, false);
        composeTimeExtras(prefix + "Time", (TimeType) type, false);
    } else if (type instanceof StringType) {
        composeStringCore(prefix + "String", (StringType) type, false);
        composeStringExtras(prefix + "String", (StringType) type, false);
    } else if (type instanceof BooleanType) {
        composeBooleanCore(prefix + "Boolean", (BooleanType) type, false);
        composeBooleanExtras(prefix + "Boolean", (BooleanType) type, false);
    } else if (type instanceof InstantType) {
        composeInstantCore(prefix + "Instant", (InstantType) type, false);
        composeInstantExtras(prefix + "Instant", (InstantType) type, false);
    } else
        throw new Error("Unhandled type");
}

Example 9 with SimpleQuantity

use of org.hl7.fhir.dstu2016may.model.SimpleQuantity in project synthea by synthetichealth.

the class FhirR4 method medicationAdministration.

/**
 * Add a MedicationAdministration if needed for the given medication.
 *
 * @param rand              Source of randomness to use when generating ids etc
 * @param personEntry       The Entry for the Person
 * @param bundle            Bundle to add the MedicationAdministration to
 * @param encounterEntry    Current Encounter entry
 * @param medication        The Medication
 * @param medicationRequest The related medicationRequest
 * @return The added Entry
 */
private static BundleEntryComponent medicationAdministration(RandomNumberGenerator rand, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Medication medication, MedicationRequest medicationRequest) {
    MedicationAdministration medicationResource = new MedicationAdministration();
    medicationResource.setSubject(new Reference(personEntry.getFullUrl()));
    medicationResource.setContext(new Reference(encounterEntry.getFullUrl()));
    Code code = medication.codes.get(0);
    String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI;
    medicationResource.setMedication(mapCodeToCodeableConcept(code, system));
    medicationResource.setEffective(new DateTimeType(new Date(medication.start)));
    medicationResource.setStatus(MedicationAdministration.MedicationAdministrationStatus.COMPLETED);
    if (medication.prescriptionDetails != null) {
        JsonObject rxInfo = medication.prescriptionDetails;
        MedicationAdministrationDosageComponent dosage = new MedicationAdministrationDosageComponent();
        // as_needed is false
        if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
            Quantity dose = new SimpleQuantity().setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
            dosage.setDose((SimpleQuantity) dose);
            if (rxInfo.has("instructions")) {
                for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
                    JsonObject instruction = instructionElement.getAsJsonObject();
                    dosage.setText(instruction.get("display").getAsString());
                }
            }
        }
        if (rxInfo.has("refills")) {
            SimpleQuantity rate = new SimpleQuantity();
            rate.setValue(rxInfo.get("refills").getAsLong());
            dosage.setRate(rate);
        }
        medicationResource.setDosage(dosage);
    }
    if (!medication.reasons.isEmpty()) {
        // Only one element in list
        Code reason = medication.reasons.get(0);
        for (BundleEntryComponent entry : bundle.getEntry()) {
            if (entry.getResource().fhirType().equals("Condition")) {
                Condition condition = (Condition) entry.getResource();
                // Only one element in list
                Coding coding = condition.getCode().getCoding().get(0);
                if (reason.code.equals(coding.getCode())) {
                    medicationResource.addReasonReference().setReference(entry.getFullUrl());
                }
            }
        }
    }
    BundleEntryComponent medicationAdminEntry = newEntry(rand, bundle, medicationResource);
    return medicationAdminEntry;
}

Example 10 with SimpleQuantity

use of org.hl7.fhir.dstu2016may.model.SimpleQuantity in project synthea by synthetichealth.

the class FhirR4 method medicationRequest.

/**
 * Map the given Medication to a FHIR MedicationRequest resource, and add it to the given Bundle.
 *
 * @param person         The person being prescribed medication
 * @param personEntry    The Entry for the Person
 * @param bundle         Bundle to add the Medication to
 * @param encounterEntry Current Encounter entry
 * @param medication     The Medication
 * @return The added Entry
 */
private static BundleEntryComponent medicationRequest(Person person, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Medication medication) {
    MedicationRequest medicationResource = new MedicationRequest();
    if (USE_US_CORE_IG) {
        Meta meta = new Meta();
        meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-medicationrequest");
        medicationResource.setMeta(meta);
    } else if (USE_SHR_EXTENSIONS) {
        medicationResource.addExtension().setUrl(SHR_EXT + "shr-base-ActionCode-extension").setValue(PRESCRIPTION_OF_DRUG_CC);
        medicationResource.setMeta(new Meta().addProfile(SHR_EXT + "shr-medication-MedicationRequested"));
        Extension requestedContext = new Extension();
        requestedContext.setUrl(SHR_EXT + "shr-action-RequestedContext-extension");
        requestedContext.addExtension(SHR_EXT + "shr-action-Status-extension", new CodeType("completed"));
        requestedContext.addExtension(SHR_EXT + "shr-action-RequestIntent-extension", new CodeType("original-order"));
        medicationResource.addExtension(requestedContext);
    }
    medicationResource.setSubject(new Reference(personEntry.getFullUrl()));
    medicationResource.setEncounter(new Reference(encounterEntry.getFullUrl()));
    Code code = medication.codes.get(0);
    String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI;
    medicationResource.setMedication(mapCodeToCodeableConcept(code, system));
    if (USE_US_CORE_IG && medication.administration) {
        // Occasionally, rather than use medication codes, we want to use a Medication
        // Resource. We only want to do this when we use US Core, to make sure we
        // sometimes produce a resource for the us-core-medication profile, and the
        // 'administration' flag is an arbitrary way to decide without flipping a coin.
        org.hl7.fhir.r4.model.Medication drugResource = new org.hl7.fhir.r4.model.Medication();
        Meta meta = new Meta();
        meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-medication");
        drugResource.setMeta(meta);
        drugResource.setCode(mapCodeToCodeableConcept(code, system));
        drugResource.setStatus(MedicationStatus.ACTIVE);
        BundleEntryComponent drugEntry = newEntry(person, bundle, drugResource);
        medicationResource.setMedication(new Reference(drugEntry.getFullUrl()));
    }
    medicationResource.setAuthoredOn(new Date(medication.start));
    medicationResource.setIntent(MedicationRequestIntent.ORDER);
    org.hl7.fhir.r4.model.Encounter encounter = (org.hl7.fhir.r4.model.Encounter) encounterEntry.getResource();
    medicationResource.setRequester(encounter.getParticipantFirstRep().getIndividual());
    if (medication.stop != 0L) {
        medicationResource.setStatus(MedicationRequestStatus.STOPPED);
    } else {
        medicationResource.setStatus(MedicationRequestStatus.ACTIVE);
    }
    if (!medication.reasons.isEmpty()) {
        // Only one element in list
        Code reason = medication.reasons.get(0);
        for (BundleEntryComponent entry : bundle.getEntry()) {
            if (entry.getResource().fhirType().equals("Condition")) {
                Condition condition = (Condition) entry.getResource();
                // Only one element in list
                Coding coding = condition.getCode().getCoding().get(0);
                if (reason.code.equals(coding.getCode())) {
                    medicationResource.addReasonReference().setReference(entry.getFullUrl());
                }
            }
        }
    }
    if (medication.prescriptionDetails != null) {
        JsonObject rxInfo = medication.prescriptionDetails;
        Dosage dosage = new Dosage();
        dosage.setSequence(1);
        // as_needed is true if present
        dosage.setAsNeeded(new BooleanType(rxInfo.has("as_needed")));
        if (rxInfo.has("as_needed")) {
            dosage.setText("Take as needed.");
        }
        // as_needed is false
        if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
            Timing timing = new Timing();
            TimingRepeatComponent timingRepeatComponent = new TimingRepeatComponent();
            timingRepeatComponent.setFrequency(rxInfo.get("dosage").getAsJsonObject().get("frequency").getAsInt());
            timingRepeatComponent.setPeriod(rxInfo.get("dosage").getAsJsonObject().get("period").getAsDouble());
            timingRepeatComponent.setPeriodUnit(convertUcumCode(rxInfo.get("dosage").getAsJsonObject().get("unit").getAsString()));
            timing.setRepeat(timingRepeatComponent);
            dosage.setTiming(timing);
            Quantity dose = new SimpleQuantity().setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
            DosageDoseAndRateComponent dosageDetails = new DosageDoseAndRateComponent();
            dosageDetails.setType(new CodeableConcept().addCoding(new Coding().setCode(DoseRateType.ORDERED.toCode()).setSystem(DoseRateType.ORDERED.getSystem()).setDisplay(DoseRateType.ORDERED.getDisplay())));
            dosageDetails.setDose(dose);
            List<DosageDoseAndRateComponent> details = new ArrayList<DosageDoseAndRateComponent>();
            details.add(dosageDetails);
            dosage.setDoseAndRate(details);
            if (rxInfo.has("instructions")) {
                String text = "";
                for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
                    JsonObject instruction = instructionElement.getAsJsonObject();
                    Code instructionCode = new Code(SNOMED_URI, instruction.get("code").getAsString(), instruction.get("display").getAsString());
                    text += instructionCode.display + "\n";
                    dosage.addAdditionalInstruction(mapCodeToCodeableConcept(instructionCode, SNOMED_URI));
                }
                dosage.setText(text);
            }
        }
        List<Dosage> dosageInstruction = new ArrayList<Dosage>();
        dosageInstruction.add(dosage);
        medicationResource.setDosageInstruction(dosageInstruction);
    }
    BundleEntryComponent medicationEntry = newEntry(person, bundle, medicationResource);
    // create new claim for medication
    medicationClaim(person, personEntry, bundle, encounterEntry, medication.claim, medicationEntry);
    // Create new administration for medication, if needed
    if (medication.administration) {
        medicationAdministration(person, personEntry, bundle, encounterEntry, medication, medicationResource);
    }
    return medicationEntry;
}